Removing rare variants from SNP array before imputation then putting them back in after imputation?
Entering edit mode
14 months ago
curious ▴ 570

I am trying to impute SNP array data on the Michigan imputation server. My overlap with the reference panel is about 60%, but is leading to some dropped chunks due to poor overlap. I plotted MAF of sites that do not overlap with reference and find that they are the rarest of the rare among all my input, so does make sense that those would be less likely to be in the reference panel. One thought I had to boost my overlap and prevent dropped chunks was to

  1. take out snps with low MAF pre-imputation, which should boost my overlap
  2. do the imputation
  3. put the snps with low MAF back in after imputation.

Is this a thing that people do? Or am I just stripping important information from my input?

imputation snp array • 314 views

Login before adding your answer.

Traffic: 1438 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6